zoonproject · goldingn · Dec 11, 2015 · Dec 7, 2015 · Dec 7, 2015 · Dec 7, 2015
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -3,9 +3,20 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 vignettes/cache
+vignettes/figure
 Notes_for_zoon_developers.md
 zoonDemo.R
 zoonQuickStart.R
 .travis.yml
 code_of_conduct.md
 vignettes/figure
+tests/testthat/*.pdf
+tests/testthat/testChangeWorkflow.R
+tests/testthat/testGetMaxEnt.R
+tests/testthat/testplot.zoonWorkflow.R
+tests/testthat/testprint.zoonSummary.R
+tests/testthat/testprint.zoonWorkflow.R
+tests/testthat/testRerunWorkflow.R
+tests/testthat/testRunModules.R
+tests/testthat/testsummary.zoonWorkflow.R
+tests/testthat/testWholeWorkflows.R
diff --git a/.gitignore b/.gitignore
@@ -9,3 +9,6 @@ vignettes/*.md
 vignettes/*.R
 vignettes/figure
 vignettes/cache
+
+# outputs from testing
+tests/testthat/*.pdf
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,24 +1,26 @@
 Package: zoon
 Type: Package
 Title: Reproducible, Accessible & Shareable Species Distribution Modelling
-Version: 0.3.3
+Version: 0.4.21
 Author: Tim Lucas, Nick Golding, Tom August, Greg McInerny, Emiel van Loon
-Maintainer: Nick Golding <[email protected]>
+Maintainer: Tom August <[email protected]>
 Description: Reproducible and remixable species distribution modelling. The
     package reads user submitted modules from an online repository, runs full
     SDM workflows and returns output that is fully reproducible.
 License: BSD_3_clause + file LICENSE
 Imports:
     RCurl,
     dismo,
-    rfigshare
+    rfigshare,
+    methods
 Depends:
     raster (>= 2.4-20),
     R (>= 3.2.0)
 Suggests:
     knitr,
-    testthat
+    testthat,
+    gam
 VignetteBuilder: knitr
 LazyData: TRUE
 URL: https://github.com/zoonproject/zoon
-RoxygenNote: 5.0.0
+RoxygenNote: 5.0.1
diff --git a/NAMESPACE b/NAMESPACE
@@ -19,5 +19,16 @@ export(ZoonPredict)
 export(workflow)
 import(RCurl)
 import(dismo)
+import(methods)
 import(raster)
+importFrom(graphics,par)
+importFrom(graphics,plot.new)
+importFrom(graphics,rect)
+importFrom(graphics,segments)
+importFrom(graphics,strwidth)
 importFrom(rfigshare,fs_new_article)
+importFrom(utils,browseURL)
+importFrom(utils,capture.output)
+importFrom(utils,download.file)
+importFrom(utils,install.packages)
+importFrom(utils,sessionInfo)
diff --git a/R/BuildModule.R b/R/BuildModule.R
@@ -28,6 +28,8 @@
 #'
 #' @return Name of the module. Outputs a file
 #' @name BuildModule
+#' @import methods
+#' @importFrom utils capture.output
 #' @export
 
 BuildModule <- function(object, type, dir='.', title = '',  description = '',

diff --git a/R/ChangeWorkflow.R b/R/ChangeWorkflow.R
@@ -12,6 +12,7 @@
 #'
 #'@export
 #'@name ChangeWorkflow
+#'@importFrom utils sessionInfo
 #'@examples \dontrun{
 #' w <- workflow(UKAnophelesPlumbeus,
 #'               UKAir,

diff --git a/R/GetPackage.R b/R/GetPackage.R
@@ -7,10 +7,8 @@
 #' @param package The name of the package with or without
 #' quotes
 #' @return NULL
-#' @examples  
-#' \dontrun{
-#' GetPackage('gam')
-#' }
+#' @importFrom utils install.packages
+#' @examples GetPackage('gam')
 #' @export
 
 GetPackage <- function (package) {

diff --git a/R/HelpFunctions.R b/R/HelpFunctions.R
@@ -39,6 +39,7 @@ ModuleHelp <- function(module){
 
 
 # Download a file with libcurl and no messages to the console
+#'@importFrom utils download.file
 
 DownloadQuietly <- function(url, file) {
   download.file(url,
@@ -52,6 +53,7 @@ DownloadQuietly <- function(url, file) {
 # Display a module helpfile in accordance with the 'help_type' option
 # help is either displayed as an HTML or text, pdf is not supported and 
 # an error is returned
+#'@importFrom utils browseURL
 
 DisplayModuleHelp <- function (url) {
 

diff --git a/R/RerunWorkflow.R b/R/RerunWorkflow.R
@@ -2,18 +2,20 @@
 #'
 #' Takes a workflow object and reruns it.
 #'
-#'@param workflow A zoonWorkflow object from a previous zoon analysis
-#'@param from Which modules should be run. If NULL (default), run from the
+#' @param workflow A zoonWorkflow object from a previous zoon analysis
+#' @param from Which modules should be run. If NULL (default), run from the
 #'  first NULL output (i.e. where the workflow broke). Otherwise takes an
 #'  integer and runs from that module.
 #'
-#'@return A list with the results of each module and a copy of the
+#' @return A list with the results of each module and a copy of the
 #'  call used to execute the workflow.
 #'
-#'@export
-#'@name RerunWorkflow
-#'@examples \dontrun{
-#' w <- workflow(UKAnophelesPlumbeus, UKAir,
+#' @export
+#' @name RerunWorkflow
+#' @importFrom utils sessionInfo
+#' @examples \dontrun{
+#' w <- workflow(UKAnophelesPlumbeus,
+#'               UKAir,
 #'               OneHundredBackground, 
 #'               LogisticRegression,
 #'               SameTimePlaceMap)

diff --git a/R/SearchFunctions.R b/R/SearchFunctions.R
@@ -5,9 +5,14 @@
 #'@return A list with all module names.
 #'@name GetModuleList
 #'@param renew Download from github even if we already have a module list.
+#' @details This function will only work on a platform that supports the 
+#' method 'libcurl' in the function url. This can be tested using the function
+#' \code{capabilities} (see example).
 #'
 #'@export
-#'@examples \dontrun{GetModuleList()}
+#'@examples 
+#'# GetModuleList requires libcurl to be supported
+#'if(capabilities('libcurl')) GetModuleList()
 
 GetModuleList <- function(renew = FALSE){
 

diff --git a/R/ZoonFigshare.R b/R/ZoonFigshare.R
@@ -18,6 +18,7 @@
 #' @param tags Character vector of searchable tags. 
 #'
 #' @importFrom rfigshare fs_new_article
+#' @importFrom utils browseURL
 #' @export
 
 ZoonFigshare <- function(zoonWorkflow, title = 'My Zoon Workflow',

diff --git a/R/plot.zoonWorkflow.R b/R/plot.zoonWorkflow.R
@@ -1,3 +1,5 @@
+#' @importFrom graphics strwidth
+
 GetCex <- function(string, width = 9) {
   # given a string (character vector of length one),
   # and a target width on screen, in user coordinates
@@ -7,6 +9,8 @@ GetCex <- function(string, width = 9) {
   return (cex)
 }
 
+#' @importFrom graphics strwidth segments
+
 ModuleLabels <- function(colr, IsChain, IsList){
   ###___ function for writing the module labels 
 
@@ -43,6 +47,7 @@ ModuleLabels <- function(colr, IsChain, IsList){
 } #END ModuleLabels
 
 
+#' @importFrom graphics rect segments strwidth
 
 Boxed2 <- function (NoOfModules, InModuleList, IsList, IsChain, ModuleNames) {
   ###___ function for writing the boxes 
@@ -226,18 +231,19 @@ CallLister <- function( callList ){
 #' @param \dots currently ignored
 #'
 #' @method plot zoonWorkflow
+#' @importFrom graphics plot.new par rect
 #' @export
 plot.zoonWorkflow <- function(x, ...) {
 
   # set up new device
   plot.new()
   par(mar = c(0, 0, 0, 0))
 
-  plot(-99, -99,
-       xlim = c(0, 110),
-       ylim = c(-100, 125),
-       xlab = "", ylab = "",
-       axes = FALSE)
+  graphics::plot(-99, -99,
+                 xlim = c(0, 110),
+                 ylim = c(-100, 125),
+                 xlab = "", ylab = "",
+                 axes = FALSE)
 
   rect( -200, -200, 200, 200,
         col = "cornsilk1",

diff --git a/R/zoon.R b/R/zoon.R
@@ -39,21 +39,22 @@ NULL
 #'   give the modules in the form of a function 
 #'   e.g. occurrence = AModule(para1 = 2, para2 = 'detail')
 #'
-#'@param occurrence Occurrence module to be used.
-#'@param covariate  Covariate module to be used.
-#'@param process Process module to be used.
-#'@param model SDM model module to be used. 
-#'@param output Output module to be used.
-#'@param forceReproducible Logical whether to force zoon to collect modules 
+#' @param occurrence Occurrence module to be used.
+#' @param covariate  Covariate module to be used.
+#' @param process Process module to be used.
+#' @param model SDM model module to be used. 
+#' @param output Output module to be used.
+#' @param forceReproducible Logical whether to force zoon to collect modules 
 #'  from the online repo. This ensure the analysis is reproducible.
 #'
-#'@return A list with the results of each module and a copy of the
+#' @return A list with the results of each module and a copy of the
 #'  code used to execute the workflow (what's there now should be source-able
 #'  though I'm sure there is a much neater approach than the one I took - the
 #'  ultimate aim would be a much nicer way of enhancing reproducibility).
-#'@export
-#'@name workflow
-#'@examples 
+#' @export
+#' @name workflow
+#' @importFrom utils sessionInfo
+#' @examples 
 #'# run a workflow, using the logistic regression model
 #'\dontrun{
 #'

diff --git a/R/zoonHelpers.R b/R/zoonHelpers.R
@@ -440,7 +440,7 @@ ErrorModule <- function(cond, mod, e){
   message()
   # Where did workflow break and where is the progress stored?
   x <- paste("Stopping workflow due to error in", module, "module.\n", 
-             "Workflow progress stored in object 'tmpZoonWorkflow'.")
+             "Workflow progress will be returned.")
   # Throw error. The call for this error is meaningless so don't print it.
   stop(x, call. = FALSE)
 }
@@ -485,6 +485,7 @@ Writeable <- function (dir) {
 #'  
 #' @export
 #' @name GetMaxEnt
+#' @importFrom utils browseURL
 GetMaxEnt <- function () {
   # Send the user to download the MaxEnt executable,
   # then find and upload it

diff --git a/inst/doc/Building_a_module.R b/inst/doc/Building_a_module.R